scPDB - 3gwd entry

Protein Data Bank Entry:

PDB ID : 3gwd

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2009-03-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclohexanone monooxygenase
ID:	C0STX7_9NOCA
AC:	C0STX7
Organism:	Rhodococcus sp. HI-31
Reign:	Bacteria
TaxID:	638919
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	41.261
Number of residues:	62
Including
Standard Amino Acids:	56
Non Standard Amino Acids:	2
Water Molecules:	4
Cofactors:	NAP NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.998	428.625

% Hydrophobic	% Polar
46.46	53.54
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	77.46 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-12.7224	3.25419	6.67628

Binding mode :

What is Poseview ?

2D View
3D View

Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C4'	CD2	PHE- 18	4.06	0	Hydrophobic	false
O1P	N	GLY- 19	2.78	156.79	H-Bond (Protein Donor)	false
O3B	OD2	ASP- 39	2.6	157.8	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 39	3.27	137.51	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 39	2.77	156.22	H-Bond (Ligand Donor)	false
N3A	N	LYS- 40	3.49	147.72	H-Bond (Protein Donor)	false
O2A	N	THR- 47	2.87	166.99	H-Bond (Protein Donor)	false
O2A	OG1	THR- 47	2.96	173.89	H-Bond (Protein Donor)	false
C2'	CG2	THR- 47	4.31	0	Hydrophobic	false
C7	CG2	THR- 47	3.88	0	Hydrophobic	false
C8	CG2	THR- 47	3.33	0	Hydrophobic	false
O2'	OG1	THR- 47	3.12	155.91	H-Bond (Ligand Donor)	false
O4'	OG1	THR- 47	3.33	160.08	H-Bond (Ligand Donor)	false
C6	CH2	TRP- 48	3.36	0	Hydrophobic	false
O3B	NE1	TRP- 50	3.18	135	H-Bond (Protein Donor)	false
O2B	NE1	TRP- 50	2.96	139.18	H-Bond (Protein Donor)	false
C7M	CB	ASN- 51	4.27	0	Hydrophobic	false
C7M	CE2	TYR- 53	3.91	0	Hydrophobic	false
O4	N	ASP- 59	2.7	131.51	H-Bond (Protein Donor)	false
N3	OG1	THR- 60	2.7	177.24	H-Bond (Ligand Donor)	false
O4	N	THR- 60	3.1	140.84	H-Bond (Protein Donor)	false
O3'	OH	TYR- 65	2.66	157.71	H-Bond (Protein Donor)	false
N6A	O	VAL- 112	2.97	174.5	H-Bond (Ligand Donor)	false
N1A	N	VAL- 112	2.9	146.23	H-Bond (Protein Donor)	false
C1'	CD1	LEU- 146	4.25	0	Hydrophobic	false
C8M	CZ	PHE- 382	3.98	0	Hydrophobic	false
C5'	CD1	LEU- 428	4.47	0	Hydrophobic	false
O2	N	LEU- 437	2.75	170.9	H-Bond (Protein Donor)	false
C3'	CD1	LEU- 437	3.8	0	Hydrophobic	false
C5'	CD1	ILE- 441	4.13	0	Hydrophobic	false
C7M	C4N	NAP- 542	3.48	0	Hydrophobic	false
O2P	O	HOH- 545	2.58	153.9	H-Bond (Protein Donor)	false
O1P	O	HOH- 546	2.72	165.38	H-Bond (Protein Donor)	false